#include <PottsMesh.hpp>

Inheritance diagram for PottsMesh< DIM >:

Collaboration diagram for PottsMesh< DIM >:

Classes
class	PottsElementIterator
Public Member Functions
PottsElementIterator	GetElementIteratorBegin (bool skipDeletedElements=true)
PottsElementIterator	GetElementIteratorEnd ()
	PottsMesh (std::vector< Node< DIM > * > nodes, std::vector< PottsElement< DIM > * > pottsElements, std::vector< std::set< unsigned > > vonNeumannNeighbouringNodeIndices, std::vector< std::set< unsigned > > mooreNeighbouringNodeIndices)
	PottsMesh ()
virtual	~PottsMesh ()
virtual unsigned	GetNumNodes () const
virtual unsigned	GetNumElements () const
unsigned	GetNumAllElements () const
PottsElement< DIM > *	GetElement (unsigned index) const
virtual c_vector< double, DIM >	GetCentroidOfElement (unsigned index)
void	ConstructFromMeshReader (AbstractMeshReader< DIM, DIM > &rMeshReader)
virtual void	Clear ()
virtual c_vector< double, DIM >	GetVectorFromAtoB (const c_vector< double, DIM > &rLocationA, const c_vector< double, DIM > &rLocationB)
virtual double	GetVolumeOfElement (unsigned index)
virtual double	GetSurfaceAreaOfElement (unsigned index)
std::set< unsigned >	GetMooreNeighbouringNodeIndices (unsigned nodeIndex)
std::set< unsigned >	GetVonNeumannNeighbouringNodeIndices (unsigned nodeIndex)
void	DeleteElement (unsigned index)
unsigned	DivideElement (PottsElement< DIM > *pElement, bool placeOriginalElementBelow=false)
unsigned	AddElement (PottsElement< DIM > *pNewElement)
Protected Member Functions
unsigned	SolveNodeMapping (unsigned index) const
unsigned	SolveElementMapping (unsigned index) const
unsigned	SolveBoundaryElementMapping (unsigned index) const
template<class Archive >
void	save (Archive &archive, const unsigned int version) const
template<class Archive >
void	load (Archive &archive, const unsigned int version)
Protected Attributes
std::vector< PottsElement< DIM > * >	mElements
std::vector< unsigned >	mDeletedElementIndices
std::vector< std::set< unsigned > >	mVonNeumannNeighbouringNodeIndices
std::vector< std::set< unsigned > >	mMooreNeighbouringNodeIndices
Friends
class	TestPottsMesh
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class PottsMesh< DIM >

A Potts-based mesh class, for use in Cellular Potts model simulations.

Definition at line 63 of file PottsMesh.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

PottsMesh< DIM >::PottsMesh	(	std::vector< Node< DIM > * >	nodes,
		std::vector< PottsElement< DIM > * >	pottsElements,
		std::vector< std::set< unsigned > >	vonNeumannNeighbouringNodeIndices,
		std::vector< std::set< unsigned > >	mooreNeighbouringNodeIndices
	)

Default constructor.

Parameters:

nodes	vector of pointers to nodes
pottsElements	vector of pointers to PottsElements
vonNeumannNeighbouringNodeIndices	vector of set of Moore Neighbours for each node
mooreNeighbouringNodeIndices	vector of set of VonNeuman Neighbours for each node

Definition at line 43 of file PottsMesh.cpp.

References EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

PottsMesh< DIM >::PottsMesh ( )

Default constructor for use by serializer.

Definition at line 89 of file PottsMesh.cpp.

template<unsigned DIM>

PottsMesh< DIM >::~PottsMesh ( ) [virtual]

Destructor.

Definition at line 96 of file PottsMesh.cpp.

Member Function Documentation

template<unsigned DIM>

unsigned PottsMesh< DIM >::AddElement ( PottsElement< DIM > * pNewElement )

Add an element to the mesh.

Parameters:

pNewElement the new element

Returns:: the index of the new element in the mesh

Definition at line 389 of file PottsMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), and MutableElement< DIM, DIM >::RegisterWithNodes().

template<unsigned DIM>

void PottsMesh< DIM >::Clear ( ) [virtual]

Delete mNodes and mElements.

Definition at line 122 of file PottsMesh.cpp.

template<unsigned DIM>

void PottsMesh< DIM >::ConstructFromMeshReader ( AbstractMeshReader< DIM, DIM > & rMeshReader )

Construct the mesh using a MeshReader.

Parameters:

rMeshReader the mesh reader

Definition at line 406 of file PottsMesh.cpp.

References ElementData::AttributeValue, AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextElementData(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumElementAttributes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), ElementData::NodeIndices, AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::Reset(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::SetAttribute().

Referenced by PottsMesh< SPACE_DIM >::load().

template<unsigned DIM>

void PottsMesh< DIM >::DeleteElement ( unsigned index )

Mark an element as deleted. Note that in a Potts mesh this does not delete the nodes so no remeshing is required.

Parameters:

index the global index of a specified Potts element

Definition at line 254 of file PottsMesh.cpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::DivideElement	(	PottsElement< DIM > *	pElement,
		bool	placeOriginalElementBelow = `false`
	)

Divide an element by assigning half the nodes to each new element in numerical order. If an odd number of nodes then the existing element has one more node than the new element.

Parameters:

pElement	the element to divide
placeOriginalElementBelow	whether to place the original element below (in the y direction) the new element (defaults to false)

Returns:: the index of the new element

Not implemented in 1d

Remove the correct nodes from each element. If placeOriginalElementBelow is true, place the original element below (in the y direction or z in 3d) the new element; otherwise, place it above.

Todo:: this could be more efficient

Definition at line 262 of file PottsMesh.cpp.

References MutableElement< DIM, DIM >::DeleteNode(), EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

c_vector< double, DIM > PottsMesh< DIM >::GetCentroidOfElement ( unsigned index ) [virtual]

Compute the centroid of an element.

This needs to be overridden in daughter classes for non-Euclidean metrics.

Parameters:

index the global index of a specified vertex element

Returns:: (centroid_x,centroid_y).

Todo:: This should probably be returning the nearest node

Definition at line 171 of file PottsMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

PottsElement< DIM > * PottsMesh< DIM >::GetElement ( unsigned index ) const

Parameters:

index the global index of a specified PottsElement.

Returns:: a pointer to the PottsElement

Definition at line 164 of file PottsMesh.cpp.

template<unsigned DIM>

PottsMesh< DIM >::PottsElementIterator PottsMesh< DIM >::GetElementIteratorBegin ( bool skipDeletedElements = true ) [inline]

Get an iterator to the first element in the mesh.

Parameters:

skipDeletedElements whether to include deleted element

Definition at line 409 of file PottsMesh.hpp.

template<unsigned DIM>

PottsMesh< DIM >::PottsElementIterator PottsMesh< DIM >::GetElementIteratorEnd ( ) [inline]

Get an iterator to one past the last element in the mesh.

Definition at line 416 of file PottsMesh.hpp.

template<unsigned DIM>

std::set< unsigned > PottsMesh< DIM >::GetMooreNeighbouringNodeIndices ( unsigned nodeIndex )

Given a node, return a set containing the indices of its Moore neighbouring nodes.

Parameters:

nodeIndex global index of the node

Returns:: neighbouring node indices in Moore neighbourhood

Definition at line 242 of file PottsMesh.cpp.

Referenced by MultipleCaBasedCellPopulation< DIM >::AddCell(), and MultipleCaBasedCellPopulation< DIM >::UpdateCellLocations().

template<unsigned DIM>

unsigned PottsMesh< DIM >::GetNumAllElements ( ) const

Returns:: the number of PottsElements in the mesh, including those marked as deleted.

Definition at line 158 of file PottsMesh.cpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::GetNumElements ( ) const [virtual]

Returns:: the number of PottsElements in the mesh.

Definition at line 152 of file PottsMesh.cpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::GetNumNodes ( ) const [virtual]

Returns:: the number of Nodes in the mesh.

Reimplemented from AbstractMesh< DIM, DIM >.

Definition at line 146 of file PottsMesh.cpp.

Referenced by PottsMeshWriter< SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned DIM>

double PottsMesh< DIM >::GetSurfaceAreaOfElement ( unsigned index ) [virtual]

Compute the surface area (or perimeter in 2D) of a PottsElement.

This needs to be overridden in daughter classes for non-Euclidean metrics.

Parameters:

index the global index of a specified PottsElement

Returns:: the surfacearea of the element

Todo:: not implemented in 3d yet

Definition at line 208 of file PottsMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

c_vector< double, DIM > PottsMesh< DIM >::GetVectorFromAtoB	(	const c_vector< double, DIM > &	rLocationA,
		const c_vector< double, DIM > &	rLocationB
	)		`[virtual]`

Overridden GetVectorFromAtoB() method. Returns a vector between two points in space.

If the mesh is being used to represent a Voronoi tessellation, and mpDelaunayMesh is not NULL, then use that to compute GetVectorFromAtoB.

Parameters:

rLocationA	a c_vector of coordinates
rLocationB	a c_vector of coordinates

Returns:: c_vector from location A to location B.

Definition at line 191 of file PottsMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB().

template<unsigned DIM>

double PottsMesh< DIM >::GetVolumeOfElement ( unsigned index ) [virtual]

Get the volume (or area in 2D, or length in 1D) of a PottsElement.

This needs to be overridden in daughter classes for non-Euclidean metrics.

Parameters:

index the global index of a specified PottsElement element

Returns:: the volume of the element

Definition at line 199 of file PottsMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

std::set< unsigned > PottsMesh< DIM >::GetVonNeumannNeighbouringNodeIndices ( unsigned nodeIndex )

Given a node, return a set containing the indices of its Von Neumann neighbouring nodes.

Parameters:

nodeIndex global index of the node

Returns:: neighbouring node indices in Von Neumann neighbourhood

Definition at line 248 of file PottsMesh.cpp.

template<unsigned DIM>

template<class Archive >

void PottsMesh< DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)		`[inline, protected]`

Loads a mesh by using PottsMeshReader and the location in ArchiveLocationInfo.

Parameters:

archive	the archive
version	the current version of this class

Definition at line 140 of file PottsMesh.hpp.

template<unsigned DIM>

template<class Archive >

void PottsMesh< DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)		const `[inline, protected]`

Archive the PottsMesh and its member variables. Note that this will write out a PottsMeshWriter file to wherever ArchiveLocationInfo has specified.

Parameters:

archive	the archive
version	the current version of this class

Definition at line 118 of file PottsMesh.hpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::SolveBoundaryElementMapping ( unsigned index ) const [protected]

Solve boundary element mapping method. This overridden method is required as it is pure virtual in the base class.

Parameters:

index the global index of the boundary element

Definition at line 116 of file PottsMesh.cpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::SolveElementMapping ( unsigned index ) const [protected]

Solve element mapping method. This overridden method is required as it is pure virtual in the base class.

Parameters:

index the global index of the element

Definition at line 109 of file PottsMesh.cpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::SolveNodeMapping ( unsigned index ) const [protected, virtual]

Solve node mapping method. This overridden method is required as it is pure virtual in the base class.

Parameters:

index the global index of the node

Implements AbstractMesh< DIM, DIM >.

Definition at line 102 of file PottsMesh.cpp.

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractMesh< DIM, DIM >.

Definition at line 108 of file PottsMesh.hpp.

Member Data Documentation

template<unsigned DIM>

std::vector<unsigned> PottsMesh< DIM >::mDeletedElementIndices [protected]

Indices of elements that have been marked as deleted. These indices can be reused when adding new elements.

Definition at line 75 of file PottsMesh.hpp.

Referenced by PottsMesh< SPACE_DIM >::load(), and PottsMesh< SPACE_DIM >::save().

template<unsigned DIM>

std::vector<PottsElement<DIM>*> PottsMesh< DIM >::mElements [protected]

Vector of pointers to PottsElements.

Definition at line 69 of file PottsMesh.hpp.

Referenced by PottsMesh< DIM >::PottsElementIterator::IsAtEnd().

template<unsigned DIM>

std::vector< std::set<unsigned> > PottsMesh< DIM >::mMooreNeighbouringNodeIndices [protected]

Vector of set of Moore Neighbours for each node.

Definition at line 81 of file PottsMesh.hpp.

Referenced by PottsMesh< SPACE_DIM >::load(), and PottsMesh< SPACE_DIM >::save().

template<unsigned DIM>

std::vector< std::set<unsigned> > PottsMesh< DIM >::mVonNeumannNeighbouringNodeIndices [protected]

Vector of set of VonNeuman Neighbours for each node.

Definition at line 78 of file PottsMesh.hpp.

Referenced by PottsMesh< SPACE_DIM >::load(), and PottsMesh< SPACE_DIM >::save().

The documentation for this class was generated from the following files:

cell_based/src/mesh/PottsMesh.hpp
cell_based/src/mesh/PottsMesh.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

template<unsigned DIM> class PottsMesh< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class PottsMesh< DIM >